Contacts of the helix formed by residues 5 - 13 (chain B) in PDB entry 5WZF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B PHE* 3.8 2.1 + - + +
4B VAL* 1.3 75.0 - - - +
6B THR* 1.3 83.9 + - - +
7B SER* 2.6 29.0 + - - +
8B PHE* 3.0 13.2 + - - +
9B TRP* 3.1 12.1 + - - -
40B VAL* 3.9 13.2 - - - +
43B GLU* 4.8 1.9 - - - +
97B VAL* 5.1 0.9 - - - +
98B ASP* 3.9 11.3 - - - +
101B SER* 4.7 0.9 + - - -
114B TYR 2.9 17.4 + - - +
115B ALA* 3.6 12.9 - - + +
116B PHE 4.9 1.2 - - - +
120B PHE* 3.5 32.9 - - + -
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Residues in contact with THR 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ASP* 1.3 80.2 + - - +
7B SER* 1.3 58.3 + - - +
9B TRP* 3.9 0.4 - - - +
10B ALA* 2.9 30.2 + - + +
40B VAL* 3.4 22.9 + - - +
43B GLU* 2.6 37.9 + - + +
44B THR* 3.5 35.7 - - - +
47B LEU* 4.0 19.1 - - + -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 2.6 23.7 + - - -
6B THR* 1.3 78.3 - - - +
8B PHE* 1.3 60.2 + - - +
10B ALA* 4.1 4.9 - - - +
11B ALA* 3.4 21.3 + - - +
17B ASP* 5.4 0.3 - - - +
19B ARG* 4.9 3.4 + - - -
47B LEU* 5.7 2.0 - - - -
115B ALA* 3.4 1.9 - - - -
116B PHE* 2.9 40.9 + - - -
117B ASP* 4.0 18.8 - - - -
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Residues in contact with PHE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.6 16.6 - - + -
5B ASP 3.0 4.9 + - - +
7B SER* 1.3 80.0 + - - +
9B TRP* 1.3 69.2 + + - +
11B ALA* 3.1 3.8 + - - +
12B LEU* 2.9 32.4 + - + +
23B ALA* 3.3 39.5 - - + -
26B LEU* 3.8 12.3 - - + -
27B TRP* 3.6 29.4 - + + -
114B TYR* 3.3 60.3 - + + +
115B ALA 4.2 0.9 - - - +
116B PHE* 3.8 22.0 - + + -
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Residues in contact with TRP 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 3.3 27.6 - - + +
5B ASP 3.1 13.8 + - - -
6B THR 3.3 1.5 + - - +
8B PHE* 1.3 77.3 - + - +
10B ALA* 1.3 58.0 + - - +
12B LEU* 3.2 18.2 + - + +
13B GLY* 2.8 28.4 + - - -
27B TRP* 3.7 39.9 - + - -
36B THR* 3.1 34.0 + - + -
40B VAL* 3.5 24.7 - - + +
41B LEU* 4.0 9.2 - - + +
44B THR* 3.6 26.7 - - + +
48B LEU* 4.5 3.1 - - - +
63B ILE* 3.7 31.6 - - + -
69B VAL* 4.2 18.4 - - + -
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 2.9 19.1 + - + +
7B SER* 4.1 4.7 - - - +
9B TRP* 1.3 76.6 - - - +
11B ALA* 1.3 62.3 + - - +
14B ASN* 3.2 29.1 + - - +
17B ASP* 4.1 7.1 - - - +
44B THR* 4.4 1.8 - - + +
47B LEU* 3.7 28.5 - - + -
48B LEU* 3.7 21.5 - - + +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER 3.4 16.1 + - - +
8B PHE 3.1 5.0 + - - +
10B ALA* 1.3 79.6 - - - +
12B LEU* 1.3 60.3 + - - +
14B ASN 3.2 8.0 - - - +
17B ASP* 3.6 26.8 + - - +
19B ARG* 4.0 7.9 - - + +
20B HIS* 2.8 26.5 + - - -
23B ALA* 3.9 10.1 - - + -
116B PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 2.9 27.4 + - + +
9B TRP* 3.7 18.8 - - + +
11B ALA* 1.3 78.9 - - - +
13B GLY* 1.3 56.6 + - - +
14B ASN 3.3 0.4 - - - -
20B HIS* 3.0 22.7 - - - -
23B ALA* 3.9 13.6 - - + +
24B LYS* 3.9 39.7 - - + +
27B TRP* 3.8 41.1 - - + +
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Residues in contact with GLY 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TRP 2.8 16.0 + - - -
10B ALA 3.9 1.3 - - - -
12B LEU* 1.3 76.4 - - - +
14B ASN* 1.3 58.7 + - - +
15B ALA 4.1 1.3 + - - -
48B LEU* 4.3 18.6 - - - +
56B ALA* 4.3 17.3 - - - +
59B ALA* 6.0 4.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il